Contacts of the helix formed by residues 43 - 67 (chain M) in PDB entry 2ZQK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 43 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M ASP* 3.0 28.8 + - - +
25M ASN* 3.0 20.8 + - - +
26M GLN 4.0 17.0 - - - +
27M LYS* 3.9 14.8 - - + +
42M LEU* 1.3 70.9 - - - +
44M ASP* 1.3 67.2 + - - +
45M ASP* 3.1 13.7 - - + +
46M VAL* 2.7 25.7 + - + +
47M VAL* 3.3 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M LYS* 3.2 29.0 + - - +
41M VAL* 5.6 1.2 - - - +
42M LEU 3.3 3.5 + - - +
43M LYS* 1.3 69.6 - - - +
45M ASP* 1.3 64.8 + - - +
47M VAL* 3.4 9.2 + - - +
48M ALA* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M LYS* 2.8 16.0 + - + +
44M ASP* 1.3 75.6 - - - +
46M VAL* 1.3 60.1 + - + +
48M ALA* 3.5 4.6 + - - +
49M ASN* 2.8 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ALA* 3.9 17.7 - - + -
25M ASN* 3.6 34.1 - - + +
42M LEU* 4.3 8.5 - - + -
43M LYS* 2.7 25.3 + - + +
45M ASP* 1.3 70.5 - - + +
47M VAL* 1.3 68.0 + - - +
49M ASN* 2.8 6.4 + - - -
50M ILE* 2.6 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M VAL* 5.7 2.5 - - + -
42M LEU* 3.8 38.8 - - + +
43M LYS 3.3 3.8 + - - +
44M ASP* 3.7 10.1 - - - +
46M VAL* 1.3 75.9 - - - +
48M ALA* 1.3 57.1 + - - +
50M ILE* 3.7 9.0 - - - +
51M GLU* 2.9 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M ASP 2.9 17.9 + - - +
45M ASP* 3.7 5.4 - - - +
47M VAL* 1.3 78.0 - - - +
49M ASN* 1.3 62.4 + - - +
51M GLU* 3.3 20.1 - - - +
52M GLU* 3.4 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M ASP 2.8 22.8 + - - +
46M VAL* 2.8 5.8 + - + +
48M ALA* 1.3 69.9 - - - +
50M ILE* 1.3 67.9 + - + +
52M GLU* 3.4 9.4 + - - +
53M GLN* 3.3 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ARG* 4.2 23.1 - - - +
15M LEU* 3.7 46.4 - - + +
16M THR* 3.9 17.7 - - - +
19M ALA* 4.2 2.7 - - + -
42M LEU* 4.2 7.0 - - + -
46M VAL* 2.6 47.4 + - + +
47M VAL* 3.7 5.6 - - - +
49M ASN* 1.3 71.6 - - + +
51M GLU* 1.3 66.7 - - - +
53M GLN* 2.8 17.5 + - - +
54M ALA* 2.8 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M GLU* 4.0 6.8 - - - +
12M ARG* 3.3 41.0 + - - -
47M VAL* 2.9 19.1 + - + +
48M ALA* 3.3 14.8 - - - +
50M ILE* 1.3 78.7 - - - +
52M GLU* 1.3 64.0 + - - +
54M ALA* 3.5 5.9 - - - +
55M LYS* 3.1 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ALA 3.4 14.5 + - - +
49M ASN* 3.7 10.1 - - - +
50M ILE 3.1 0.4 - - - -
51M GLU* 1.3 74.1 - - - +
53M GLN* 1.3 62.2 + - + +
55M LYS* 2.8 38.5 + - - +
56M ALA* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M THR* 4.3 2.8 - - - +
15M LEU* 3.5 35.3 - - + +
49M ASN* 3.3 27.9 + - - +
50M ILE* 2.8 20.2 + - - +
52M GLU* 1.3 74.6 - - - +
54M ALA* 1.3 64.0 + - - +
56M ALA* 3.0 9.6 + - - +
57M ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M GLU* 3.5 33.9 - - + +
11M THR* 3.7 14.9 - - + +
12M ARG* 3.9 30.7 - - + +
50M ILE* 2.8 14.7 + - + +
51M GLU* 3.5 10.3 - - - +
53M GLN* 1.3 74.1 - - - +
55M LYS* 1.3 61.8 + - - +
57M ALA* 3.3 4.3 + - - +
58M GLY 3.1 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M GLU* 3.6 20.9 - - - +
51M GLU* 3.1 29.8 + - - +
52M GLU* 2.8 41.6 + - - +
54M ALA* 1.3 75.2 - - - +
56M ALA* 1.3 60.9 + - - +
58M GLY* 3.2 2.2 + - - +
59M GLU* 3.0 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLU 2.8 12.2 + - - +
53M GLN* 3.0 11.4 + - - +
55M LYS* 1.3 73.2 - - - +
57M ALA* 1.3 60.5 + - - +
59M GLU* 3.4 5.9 + - - +
60M GLU* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M THR* 3.2 20.2 - - + +
11M THR* 3.3 29.6 - - + +
53M GLN 3.0 11.5 + - - +
54M ALA 3.4 9.2 - - - +
56M ALA* 1.3 77.2 - - - +
58M GLY* 1.3 63.0 + - - +
60M GLU* 3.4 11.2 + - - +
61M ALA 3.0 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M SER* 4.6 10.1 + - - -
7M THR* 4.0 10.0 - - - +
8M GLU* 4.3 13.0 - - - -
54M ALA 3.1 10.7 + - - -
55M LYS* 3.2 4.2 + - - -
56M ALA 3.1 0.2 - - - -
57M ALA* 1.3 77.6 - - - +
59M GLU* 1.3 63.4 + - - +
61M ALA* 3.0 6.1 + - - +
62M LYS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M LYS* 3.0 23.3 + - + +
56M ALA* 4.0 5.6 - - - +
58M GLY* 1.3 76.0 - - - +
60M GLU* 1.3 54.6 + - - +
62M LYS* 3.0 33.0 + - - +
63M GLN* 2.6 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M ALA 2.9 20.0 + - - +
57M ALA* 3.5 9.3 - - - +
58M GLY 3.2 0.2 - - - -
59M GLU* 1.3 76.8 - - - +
61M ALA* 1.3 57.9 + - - +
63M GLN* 4.3 5.0 - - - +
64M GLN* 2.8 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M SER* 4.9 4.7 - - - +
7M THR* 3.5 25.6 - - + +
57M ALA 3.0 13.4 + - - +
58M GLY 3.2 9.4 - - - +
59M GLU 3.0 0.6 - - - -
60M GLU* 1.3 76.9 - - - +
62M LYS* 1.3 66.6 + - - +
64M GLN* 3.1 8.7 + - - +
65M ALA* 2.9 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M GLY 2.9 12.2 + - - +
59M GLU* 3.5 33.2 + - - +
61M ALA* 1.3 77.3 - - - +
63M GLN* 1.3 65.2 + - - +
65M ALA* 3.2 7.0 + - + +
66M ILE* 3.0 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M GLU* 2.6 23.4 + - + +
60M GLU* 4.3 4.7 - - - +
62M LYS* 1.3 77.0 - - - +
64M GLN* 1.3 61.6 + - - +
66M ILE* 3.3 25.6 + - - +
67M GLU* 3.1 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M GLU* 2.8 42.3 + - - +
61M ALA* 3.1 9.3 + - - +
63M GLN* 1.3 75.2 - - - +
65M ALA* 1.3 58.3 + - - +
67M GLU* 3.2 16.8 + - + +
68M ASN* 2.7 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M ALA 2.9 12.5 + - - +
62M LYS* 3.7 9.6 - - + +
64M GLN* 1.3 76.1 - - - +
66M ILE* 1.3 63.6 + - + +
68M ASN* 3.2 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M LYS* 3.0 36.2 + - + +
63M GLN* 3.6 29.8 - - - +
65M ALA* 1.3 72.9 - - + +
67M GLU* 1.3 55.0 + - + +
68M ASN 2.6 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M GLN* 3.1 37.4 + - - +
64M GLN* 3.2 10.6 + - + +
66M ILE* 1.3 74.1 - - + +
68M ASN* 1.3 77.1 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il